proteins Flashcards
(20 cards)
What are the amino acids that differ from each other by a single methyl or methylene group ?
- Glycine and Alanine
- Serine and Threonine
- Valine, Leucine and Isoleucine
- Asparagine and Glutamine
- Aspartate and Glutamate
Glutamate, a 5-carbon amino acid, is the precursor of three other amino acids that contain a 5-carbon chain. Identify these amino acids?
- Arginine
- Glutamine
- Proline
The 20 standard amino acids are called α-amino acids. Certain
β-amino acids are found in nature. Draw the structure of β-alanine
(3-amino-n-propionate).
+ H3N—CH —CH —COO -
Taurine (2-aminoethanesulfonic acid) is sometimes called an amino
acid.
Taurine lacks a carboxylate group at the carbon atom where the amino group is attached.
(b) Taurine is derived from cysteine. The ulfhydryl group of the Cys side chain has been oxidized to a sulfonic acid group, and the -carboxylate group has been removed.
Calculate the number of possible pentapeptides that contain one residue each Alanine, Glycine, Histidine, Lysine and Valine?
N = 1 x 2 x 3 x 4 x 5 = 120
Identify the bond donor and acceptor groups in asparagine?
Hydrogen bond donors: alpha-amino group, amide nitrogen.
Hydrogen bond acceptors: alpha-carboxylate group, amide carbonyl.
In some proteins, the side chain of serine appears to undergo ionization. Explain why ionization would be facilitated by the presence of an aspirate residue neraby ?
- The negatively charged aspartate ¬COO- group helps “pull” a hydrogen ion from the hydroxyl group of the serine side chain.
- under the correct conditions the negative charge on the aspartic acid residue can function as a base and accept the hydrogen from the hydroxyl group on the serine residue.
A sample of the amino acid tyrosine is barely soluble in water. Would a polypeptide containing only Tyrosine residues, poly[Tyr], be more or less soluble, assuming the total number of Tyr groups remains constant?
The polypeptide would be even less soluble than free Tyr, because most of the amino and carboxylate groups that interact with water and make Tyr at least slightly soluble are lost in forming the peptide bonds in poly[Tyr].
What is the net charge at neutral pH of a tripeptide containing only alanine? How does the total number of negative and positive charges change following hydrolysis of the tripeptide?
- The net charge is zero [the N-terminus is positively charged and the C-terminus is negatively charged].
- The tripeptide has one positive and one negative charge. Hydrolysis increases the total number of charges to 6: one positively charged ammonium group and one negatively charged carboxylate group for each of the three Alanines.
- Patients with Parkinson’s disease are sometimes given L-DOPA
(3,4-dihydroxyphenylalanine). What neurotransmitter is produced by
the decarboxylation of L-DOPA?
Dopamine is formed by the decarboxylation of L-DOPA by aromatic l-amino acid decarboxylase (AADC).
Over time, the glutamine residues of polypeptides are susceptible
to deamidation, a reaction in which the amide group is replaced by
a carboxylate group. What amino acid is produced when glutamine is
deamidated?
As a free amino acid, or as the N-terminal residue of a peptide or protein, glutamine deamidates readily to form pyroglutamic acid (5-oxoproline)
Which amino acids have side chains that are capable of forming isopeptide bonds?
Isopeptide bonds are intramolecular covalent bonds that form autocatalytically between the side chains of lysine and asparagine/aspartic acid
A sample of the amino acid tyrosine is barely soluble in water.
Would a polypeptide containing only Tyr residues, poly(Tyr), be more
or less soluble, assuming the total number of Tyr groups remains constant?
The polypeptide would be even less soluble than free Tyr, because most of the amino and carboxylate groups that interact with water and make Tyr at least slightly soluble are lost in forming the peptide ponds in poly(Tyr)
Indicate whether the following familiar objects are chiral or non chiral
a) a glove
b) a tennis ball
c) a screw
d) this page
e) a snowflake
f) spiral staircase
g) a shoe
a) chiral
b) non chiral
c) chiral
d) chiral
e) non chiral
f) chiral
g) chiral
how to break disulfide bonds
we use a thiol
-thiol has an electron source (such as NADPH) can break apart the disulfide bond by donating an electron
GFP synthesis
cyclization of the protein backbone which is rarely seen
-and it fits inside a beta-barrel
Relationship between the Titration Curve and the
Acid-Base Properties of Glycine
(a) Glycine is present predominantly as the species +H3NOCH2OCOOH.
(b) The average net charge of glycine is + 1/2.
(c) Half of the amino groups are ionized.
(d) The pH is equal to the pKa of the carboxyl group.
(e) The pH is equal to the pKa of the protonated amino
group.
(f) Glycine has its maximum buffering capacity.
(g) The average net charge of glycine is zero.
(h) The carboxyl group has been completely titrated
(first equivalence point).
(i) Glycine is completely titrated (second equivalence
point).
(j) The predominant species is +H3NOCH2OCOO-.
(k) The average net charge of glycine is +1.
(l) Glycine is present predominantly as a 50:50 mixture
of +H3NOCH2OCOOH and +H3NOCH2OCOO-.
(m) This is the isoelectric point.
(n) This is the end of the titration.
(o) These are the worst pH regions for buffering power
Separation of Amino Acids by Ion-Exchange Chromatography
1) ionic attraction between the _OSO3- residues on the column and positively
charged functional groups on the amino acids,(2) hydrophobic interactions between amino acid side chains and
the strongly hydrophobic backbone of the polystyrene resin.
For each pair of amino acids listed, determine which will be
eluted first from an ion-exchange column using a pH 7.0 buffer
asp and lys
arg and met
glu and val
gly and leu
ser and ala
Isoelectric Point of Pepsin
One subunit of 326 amino acids comprises pepsin, which has a molecular weight of 34,509.83g and an isoelectric point of 3.24
Isoelectric Point of Histones
The isoelectric point for H1 histone in 6.25 m urea solution in the presence of a nitrogen atmosphere was 8.90, and the corresponding values for H3, H2B, H2A, and H4 histones were 9.80, 9.90, 10.10, and 10.25, respectively.
